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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.31

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-10-21, 16:32 CDT based on data in:
        • /project/lbarreiro/USERS/austin/slamseq/data/fastp_reports
        • /project/lbarreiro/USERS/austin/slamseq/logs/hisat-3n

        General Statistics

        Showing 40/40 rows and 6/10 columns.
        Sample Name% Aligned% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% AdapterMean R1 LengthMean R2 Length
        LB-HT-28s-HT-01_S1_L005
        28.7%
        95.6%
        22913.9Mb
        156.9M
        47.1%
        98.5%
        18.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-01_S1_L008
        28.5%
        95.5%
        22701.2Mb
        155.5M
        47.0%
        98.4%
        18.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-02_S2_L005
        25.6%
        94.9%
        20615.2Mb
        140.2M
        48.5%
        98.3%
        11.5%
        158.0bp
        158.0bp
        LB-HT-28s-HT-02_S2_L006
        24.5%
        94.8%
        20624.8Mb
        140.5M
        48.5%
        98.3%
        11.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-05_S5_L005
        27.7%
        92.9%
        18164.4Mb
        126.0M
        52.9%
        97.0%
        10.5%
        158.0bp
        158.0bp
        LB-HT-28s-HT-05_S5_L006
        26.4%
        92.8%
        18158.4Mb
        126.2M
        52.9%
        96.9%
        10.5%
        158.0bp
        158.0bp
        LB-HT-28s-HT-06_S6_L005
        30.5%
        95.7%
        20473.0Mb
        140.6M
        46.1%
        98.5%
        21.3%
        158.0bp
        158.0bp
        LB-HT-28s-HT-06_S6_L007
        29.3%
        95.4%
        20196.5Mb
        139.0M
        46.1%
        98.5%
        21.3%
        158.0bp
        158.0bp
        LB-HT-28s-HT-06_S6_L008
        30.0%
        95.6%
        20008.1Mb
        137.5M
        46.0%
        98.4%
        21.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-07_S7_L006
        30.5%
        95.0%
        22843.6Mb
        155.5M
        48.7%
        98.1%
        12.5%
        158.0bp
        158.0bp
        LB-HT-28s-HT-07_S7_L008
        31.7%
        95.0%
        22603.7Mb
        153.7M
        48.7%
        98.0%
        12.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-08_S8_L005
        35.1%
        95.3%
        18472.5Mb
        124.8M
        48.2%
        98.1%
        10.8%
        158.0bp
        158.0bp
        LB-HT-28s-HT-08_S8_L007
        33.8%
        95.0%
        18301.2Mb
        123.9M
        48.2%
        98.0%
        10.8%
        158.0bp
        158.0bp
        LB-HT-28s-HT-08_S8_L008
        34.8%
        95.2%
        18366.3Mb
        124.1M
        48.1%
        98.0%
        10.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-09_S9_L005
        27.3%
        93.7%
        23039.9Mb
        160.1M
        51.2%
        97.3%
        16.1%
        158.0bp
        158.0bp
        LB-HT-28s-HT-09_S9_L006
        26.1%
        93.6%
        23083.8Mb
        160.7M
        51.1%
        97.3%
        16.1%
        158.0bp
        158.0bp
        LB-HT-28s-HT-10_S10_L005
        31.1%
        94.2%
        16183.3Mb
        109.5M
        49.8%
        97.7%
        4.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-10_S10_L007
        30.0%
        93.9%
        15994.5Mb
        108.5M
        49.7%
        97.7%
        4.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-10_S10_L008
        30.9%
        94.1%
        16052.0Mb
        108.7M
        49.7%
        97.6%
        4.5%
        158.0bp
        158.0bp
        LB-HT-28s-HT-12_S12_L005
        24.5%
        94.7%
        16895.4Mb
        113.8M
        48.4%
        98.1%
        5.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-16_S16_L008
        24.1%
        93.7%
        14598.5Mb
        99.7M
        51.1%
        97.4%
        7.6%
        158.0bp
        158.0bp
        LB-HT-28s-HT-17_S17_L005
        75.0%
        0.0%
        62.3%
        0.0Mb
        0.0M
        60.8%
        20.0%
        0.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-17_S17_L006
        50.0%
        0.0%
        83.7%
        0.0Mb
        0.0M
        52.8%
        20.0%
        0.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-17_S17_L007
        0.0%
        0.0%
        0.0Mb
        0.0M
        0.0%
        0.0%
        0.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-17_S17_L008
        0.0%
        0.0%
        48.7%
        0.0Mb
        0.0M
        61.1%
        10.0%
        0.0%
        158.0bp
        158.0bp
        LB-HT-28s-HT-18_S18_L005
        25.0%
        93.9%
        14253.1Mb
        97.0M
        50.0%
        97.6%
        6.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-18_S18_L006
        23.9%
        93.8%
        14241.7Mb
        97.0M
        50.0%
        97.5%
        6.2%
        158.0bp
        158.0bp
        LB-HT-28s-HT-18_S18_L008
        24.9%
        93.9%
        14188.8Mb
        96.6M
        49.9%
        97.5%
        6.1%
        158.0bp
        158.0bp
        LB-HT-28s-JL-02_S20_L006
        23.8%
        95.5%
        19412.0Mb
        132.1M
        46.2%
        98.5%
        13.4%
        158.0bp
        158.0bp
        LB-HT-28s-JL-04_S22_L006
        20.1%
        95.2%
        20403.2Mb
        139.8M
        47.8%
        98.5%
        14.4%
        158.0bp
        158.0bp
        LB-HT-28s-JL-04_S22_L008
        20.9%
        95.3%
        20060.8Mb
        137.3M
        47.8%
        98.4%
        14.1%
        158.0bp
        158.0bp
        LB-HT-28s-JL-06_S24_L006
        42.2%
        95.5%
        19015.0Mb
        131.9M
        47.0%
        98.1%
        18.8%
        158.0bp
        158.0bp
        LB-HT-28s-JL-06_S24_L007
        42.5%
        95.5%
        18776.0Mb
        130.3M
        47.0%
        98.1%
        18.7%
        158.0bp
        158.0bp
        LB-HT-28s-JL-06_S24_L008
        43.7%
        95.6%
        18661.7Mb
        129.2M
        46.9%
        98.0%
        18.4%
        158.0bp
        158.0bp
        LB-HT-28s-JL-07_S25_L006
        33.1%
        95.0%
        23942.1Mb
        163.9M
        48.4%
        98.0%
        12.2%
        158.0bp
        158.0bp
        LB-HT-28s-JL-08_S26_L005
        25.8%
        95.6%
        19320.8Mb
        131.6M
        46.2%
        98.7%
        13.3%
        158.0bp
        158.0bp
        LB-HT-28s-JL-08_S26_L007
        24.9%
        95.4%
        19124.5Mb
        130.5M
        46.2%
        98.6%
        13.2%
        158.0bp
        158.0bp
        LB-HT-28s-JL-08_S26_L008
        25.6%
        95.5%
        19171.1Mb
        130.6M
        46.1%
        98.5%
        13.0%
        158.0bp
        158.0bp
        LB-HT-28s-JL-09_S27_L005
        32.1%
        95.7%
        24095.5Mb
        165.1M
        46.8%
        98.4%
        14.8%
        158.0bp
        158.0bp
        LB-HT-28s-JL-09_S27_L007
        30.9%
        95.5%
        23906.6Mb
        164.1M
        46.7%
        98.3%
        14.8%
        158.0bp
        158.0bp

        HISAT2

        Maps DNA or RNA reads against a genome or a population of genomes.URL: https://ccb.jhu.edu/software/hisat2DOI: 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        Created with MultiQC

        fastp

        Version: 1.0.1

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        fastp1.0.1

        MultiQC v1.31 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.